Full experimental information, including previous experiments and timeline, can be found at the MCP website
library(phyloseq)
library(reshape2)
library(tidyverse)
library(vegan)
library(HTSSIP)
library(ape)
library(CoDaSeq)
library(philr)
library(ggtree)
library(cowplot)
library(ggplot2)
library(viridis)
library(phytools)
Full gas data for the entire experiment can be found at the Experiment 4 highcharts website
x<-read.csv(file='/Users/oliviaahern/Documents/R/Exp4/22Apr22/Exp4_Chemostat.csv',header=TRUE)
timec=x$Time..d.
mc1cO2c=x$CO2.MC1....
mc2cO2c=x$CO2.MC2....
mc3cO2c=x$CO2.MC3....
mc4cO2c=x$CO2.MC4....
mc5cO2c=x$CO2.MC5....
mc6cO2c=x$CO2.MC6....
mc1O2c=x$O2.MC1....
mc2O2c=x$O2.MC2....
mc3O2c=x$O2.MC3....
mc4O2c=x$O2.MC4....
mc5O2c=x$O2.MC5....
mc6O2c=x$O2.MC6....
x<-read.csv(file='/Users/oliviaahern/Documents/R/Exp4/22Apr22/Exp4_Batch.csv',header=TRUE)
time=x$Time..d.
mc1cO2=x$CO2.MC1....
mc2cO2=x$CO2.MC2....
mc3cO2=x$CO2.MC3....
mc4cO2=x$CO2.MC4....
mc5cO2=x$CO2.MC5....
mc6cO2=x$CO2.MC6....
mc1O2=x$O2.MC1....
mc2O2=x$O2.MC2....
mc3O2=x$O2.MC3....
mc4O2=x$O2.MC4....
mc5O2=x$O2.MC5....
mc6O2=x$O2.MC6....
par(mfrow=c(2,2),mar=c(5,5,1,1))
layout(matrix(c(1,2,2,3,4,4), nrow = 2, ncol = 3, byrow = TRUE))
plot(time,mc1O2, type='l',pch=21, col='gray70',ylim=c(20.8,21.2),
xlab="Time (days)", lwd=1, cex.axis=1.5,cex.lab = 1.5,
ylab="Oxygen (%)", yaxt='n')
axis(2, at=c(20.8, 21, 21.2), cex.axis=1.5)
lines(time, mc2O2, type='l', pch=21, col='#a44f9a')
lines(time, mc3O2, type='l', pch=21, col='#6870c8')
lines(time, mc4O2, type='l', pch=21, col='#56ae6c')
lines(time, mc5O2, type='l', pch=21, col='#af953c')
lines(time, mc6O2, type='l', pch=21, col='#ba4a4f')
plot(timec,mc1O2c, type='l',pch=21, col='gray70',ylim=c(20.5,21),
xlab="Time (days)", lwd=1,cex.axis=1.5,cex.lab = 1.5,
ylab="Oxygen (%)", yaxt="n")
axis(2, at=c(20.6, 20.8,21), cex.axis=1.5)
lines(timec, mc2O2c, type='l', pch=21, col='#a44f9a')
lines(timec, mc3O2c, type='l', pch=21, col='#6870c8')
lines(timec, mc4O2c, type='l', pch=21, col='#56ae6c')
lines(timec, mc5O2c, type='l', pch=21, col='#af953c')
lines(timec, mc6O2c, type='l', pch=21, col='#ba4a4f')
plot(time,mc1cO2, type='l',pch=21, col='gray70',ylim=c(0,0.2),
xlab="Time (days)", lwd=1,cex.axis=1.5,cex.lab = 1.5,
ylab="Carbon Dioxide (%)", yaxt='n')
axis(2, at=c(0,0.1,0.2), cex.axis=1.5)
lines(time, mc2cO2, type='l', pch=21, col='#a44f9a')
lines(time, mc3cO2, type='l', pch=21, col='#6870c8')
lines(time, mc4cO2, type='l', pch=21, col='#56ae6c')
lines(time, mc5cO2, type='l', pch=21, col='#af953c')
lines(time, mc6cO2, type='l', pch=21, col='#ba4a4f')
plot(timec,mc1cO2c, type='l',pch=21, col='gray70',ylim=c(0.18,0.3),
xlab="Time (days)", lwd=1,cex.axis=1.5,cex.lab = 1.5,
ylab="Carbon Dioxide (%)", yaxt="n")
axis(2, at=c(0.2, 0.25,0.3), cex.axis=1.5)
lines(timec, mc2cO2c, type='l', pch=21, col='#a44f9a')
lines(timec, mc3cO2c, type='l', pch=21, col='#6870c8')
lines(timec, mc4cO2c, type='l', pch=21, col='#56ae6c')
lines(timec, mc5cO2c, type='l', pch=21, col='#af953c')
lines(timec, mc6cO2c, type='l', pch=21, col='#ba4a4f')
Atomic % 13C was measured from dried GFF filters. Calculations and measurements were carried out by the MBL Stable Isotope
read=read.csv(file="/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/SIP_Spins/atomic_C_30Aug22.csv",header=T)
read1=subset(read, B_C=="B")
MC1=subset(read1, MC=="MC1")
MC2=subset(read1, MC=="MC2")
MC3=subset(read1, MC=="MC3")
MC4=subset(read1, MC=="MC4")
MC5=subset(read1,MC=="MC5")
MC6=subset(read1,MC=="MC6")
read2=subset(read, B_C=="C")
MC1c=subset(read2, MC=="MC1")
MC2c=subset(read2, MC=="MC2")
MC3c=subset(read2, MC=="MC3")
MC4c=subset(read2, MC=="MC4")
MC5c=subset(read2,MC=="MC5")
MC6c=subset(read2,MC=="MC6")
{par(mar=c(5,5,1,1), mfrow=c(1,2))
plot(MC1$TP,MC1$mm_atomic_C, type='o', ylim=c(0,10542.03827),pch=21,bg='gray70',
xlab="Time (days)", ylab="Atomic %13C", cex=1.5, cex.lab=1.4)
lines(MC1$TP, MC2$mm_atomic_C, type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.5)
lines(MC1$TP, MC3$mm_atomic_C, type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.5)
lines(MC1$TP, MC4$mm_atomic_C, type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.5)
lines(MC1$TP, MC5$mm_atomic_C, type="o", col="#af953c", bg="#af953c", pch=21,cex=1.5)
lines(MC1$TP, MC6$mm_atomic_C, type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.5)
legend('topleft',legend=c("MC1-C12", "MC2-Met", "MC3-Eth", "MC4-Ace",
"MC5-Glu", "MC6-Xyl"), bty='n', pch =21,
pt.bg=c("gray70", "#a44f9a", "#6870c8", "#56ae6c", "#af953c", "#ba4a4f"))
plot(MC1c$TP,MC1c$mm_atomic_C, type='o', ylim=c(0,13424.45736),pch=21,bg='gray70',
xlab="Time (days)", ylab="Atomic %13C", cex=1.5, cex.lab=1.4)
lines(MC1c$TP, MC2c$mm_atomic_C, type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.5)
lines(MC1c$TP, MC3c$mm_atomic_C, type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.5)
lines(MC1c$TP, MC4c$mm_atomic_C, type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.5)
lines(MC1c$TP, MC5c$mm_atomic_C, type="o", col="#af953c", bg="#af953c", pch=21,cex=1.5)
lines(MC1c$TP, MC6c$mm_atomic_C, type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.5)
legend('topleft',legend=c("MC1-C12", "MC2-Met", "MC3-Eth", "MC4-Ace",
"MC5-Glu", "MC6-Xyl"), bty='n', pch =21,
pt.bg=c("gray70", "#a44f9a", "#6870c8", "#56ae6c", "#af953c", "#ba4a4f"))
}
Atomic % 13C was measured from dried GFF filters. Calculations and measurements were carried out by the MBL Stable Isotope. POC was normalized to the amount of water filtered through each sample.
{#par(mar=c(5,5,1,1), mfrow=c(2,2))
layout(matrix(c(1,2,2,3,4,4), nrow = 2, ncol = 3, byrow = TRUE))
plot(MC1$TP,MC1$Balanced_Atomic_.13C, type='o', ylim=c(0,30),pch=21,bg='gray70',
xlab="Time (days)", ylab="Atomic %13C", cex=1.2, cex.lab=1.2,
yaxt='n')
axis(2,at=c(0,10,20,30))
lines(MC1$TP, MC2$Balanced_Atomic_.13C, type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.2)
lines(MC1$TP, MC3$Balanced_Atomic_.13C, type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.2)
lines(MC1$TP, MC4$Balanced_Atomic_.13C, type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.2)
lines(MC1$TP, MC5$Balanced_Atomic_.13C, type="o", col="#af953c", bg="#af953c", pch=21,cex=1.2)
lines(MC1$TP, MC6$Balanced_Atomic_.13C, type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.2)
# legend('topleft',legend=c("MC1-C12", "MC2-Met", "MC3-Eth", "MC4-Ace",
# "MC5-Glu", "MC6-Xyl"), bty='n', pch =21,
# pt.bg=c("gray70", "#a44f9a", "#6870c8", "#56ae6c", "#af953c", "#ba4a4f"))
plot(MC1c$TP,MC1c$Balanced_Atomic_.13C, type='o', ylim=c(0,30),pch=21,bg='gray70',
xlab="Time (days)", ylab="Atomic %13C", cex=1.2, cex.lab=1.2,
yaxt='n')
axis(2,at=c(0,10,20,30))
lines(MC1c$TP, MC2c$Balanced_Atomic_.13C, type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.2)
lines(MC1c$TP, MC3c$Balanced_Atomic_.13C, type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.2)
lines(MC1c$TP, MC4c$Balanced_Atomic_.13C, type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.2)
lines(MC1c$TP, MC5c$Balanced_Atomic_.13C, type="o", col="#af953c", bg="#af953c", pch=21,cex=1.2)
lines(MC1c$TP, MC6c$Balanced_Atomic_.13C, type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.2)
#legend('topleft',legend=c("MC1-C12", "MC2-Met", "MC3-Eth", "MC4-Ace",
# "MC5-Glu", "MC6-Xyl"), bty='n', pch =21,
# pt.bg=c("gray70", "#a44f9a", "#6870c8", "#56ae6c", "#af953c", "#ba4a4f"))
plot(MC1$TP,MC1$POC.._M., type='o', ylim=c(0,500),pch=21,bg='gray70',
xlab="Time (days)", ylab="POC (uM)", cex=1.2, cex.lab=1.2,
yaxt='n')
axis(2,at=c(0,250,500))
lines(MC1$TP, MC2$POC.._M., type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.2)
lines(MC1$TP, MC3$POC.._M., type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.2)
lines(MC1$TP, MC4$POC.._M., type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.2)
lines(MC1$TP, MC5$POC.._M., type="o", col="#af953c", bg="#af953c", pch=21,cex=1.2)
lines(MC1$TP, MC6$POC.._M., type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.2)
plot(MC1c$TP,MC1c$POC.._M., type='o', ylim=c(0,1100),pch=21,bg='gray70',
xlab="Time (days)", ylab="POC (uM)", cex=1.2, cex.lab=1.2,
yaxt='n')
axis(2,at=c(0,500,1000))
lines(MC1c$TP, MC2c$POC.._M., type="o", col="#a44f9a", bg="#a44f9a", pch=21,cex=1.2)
lines(MC1c$TP, MC3c$POC.._M., type="o", col="#6870c8", bg="#6870c8", pch=21,cex=1.2)
lines(MC1c$TP, MC4c$POC.._M., type="o", col="#56ae6c", bg="#56ae6c", pch=21,cex=1.2)
lines(MC1c$TP, MC5c$POC.._M., type="o", col="#af953c", bg="#af953c", pch=21,cex=1.2)
lines(MC1c$TP, MC6c$POC.._M., type="o", col="#ba4a4f", bg="#ba4a4f", pch=21,cex=1.2)
}
SIP gradients were setup using a CsTFA gradient centered at ~1.80 g/mL, formamide, and between 750-500 ng of RNA. Samples were spun using an ultracentrifuge spinning at 65,000 rpm at 20C for 65 hours.
Correction factors include Lueder’s Buoyant density (Lueders et al, 2010) and the Buckley Lab RNA SIP protocol.
Standard deviation between SIP runs (as of Sept 9th, 2022) were:
C13 peak was about 0.016 g/mL higher than the 13C peak.
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
dim(read)
## [1] 343 14
MC1_T2.5=subset(read, read$MC=="MC1" & TP =="2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP =="3.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP =="4.5")
## Colors
# MC1 - gray 70
# MC2 #a44f9a
# MC3 #6870c8
# MC4 #56ae6c
# MC5 #af953c
# MC6 #ba4a4f
# C12-T2.5 and 3.5
par(mfrow=c(1,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", pch=22, bg="gray70")
lines(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=23)
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg=c("gray70", "gray70"), bty='n', cex=1)
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,3.75))
lines(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", pch=22, bg="gray70")
lines(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=23)
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg=c("gray70", "gray70"), bty='n', cex=1)
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T2.5$Lueders_BD, MC2_T2.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,3.2))
lines(MC2_T2.5$Lueders_BD, MC2_T2.5$Ribo_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T3.5$Lueders_BD, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T3.5$Lueders_BD, MC2_T3.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T4.5$Lueders_BD, MC2_T4.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topleft", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,4.6))
lines(MC2_T4.5$Lueders_BD, MC2_T4.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topleft", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC2_T2.5$Lueders_BD, MC2_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#a44f9a',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#a44f9a")
lines(MC2_T3.5$Lueders_BD, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Lueders_BD, MC2_T4.5$Ribo_RMAX,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topleft", legend=c("MC2-Met-T2.5","MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a"), bty='n')
plot(MC2_T2.5$Lueders_BD, MC2_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#a44f9a',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#a44f9a")
lines(MC2_T3.5$Lueders_BD, MC2_T3.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Lueders_BD, MC2_T4.5$Ribo_conc,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topleft", legend=c("MC2-Met-T2.5","MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a"), bty='n')
}
# MC1-T2.5 and MC3-Eth-T2.5
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T2.5$Lueders_BD, MC3_T2.5$Ribo_RMAX,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC3_T2.5$Lueders_BD, MC3_T2.5$Ribo_conc,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T3.5$Lueders_BD, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T3.5$Lueders_BD, MC3_T3.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T4.5$Lueders_BD, MC3_T4.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topleft", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1.2))
lines(MC3_T4.5$Lueders_BD, MC3_T4.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topleft", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC3_T2.5$Lueders_BD, MC3_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#6870c8',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#6870c8")
lines(MC3_T3.5$Lueders_BD, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Lueders_BD, MC3_T4.5$Ribo_RMAX,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topleft", legend=c("MC3-Eth-T2.5","MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8"), bty='n')
plot(MC3_T2.5$Lueders_BD, MC3_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#6870c8',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#6870c8")
lines(MC3_T3.5$Lueders_BD, MC3_T3.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Lueders_BD, MC3_T4.5$Ribo_conc,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topleft", legend=c("MC3-Eth-T2.5","MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8"), bty='n')
}
######
# MC1 - T2.5 vs. MC4 - Ace
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T2.5$Lueders_BD, MC4_T2.5$Ribo_RMAX,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC4_T2.5$Lueders_BD, MC4_T2.5$Ribo_conc,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T3.5$Lueders_BD, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T3.5$Lueders_BD, MC4_T3.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T4.5$Lueders_BD, MC4_T4.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topleft", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,0.7))
lines(MC4_T4.5$Lueders_BD, MC4_T4.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topleft", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC4_T2.5$Lueders_BD, MC4_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#56ae6c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#56ae6c")
lines(MC4_T3.5$Lueders_BD, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Lueders_BD, MC4_T4.5$Ribo_RMAX,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topleft", legend=c("MC4-Ace-T2.5","MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c"), bty='n')
plot(MC4_T2.5$Lueders_BD, MC4_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#56ae6c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#56ae6c")
lines(MC4_T3.5$Lueders_BD, MC4_T3.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Lueders_BD, MC4_T4.5$Ribo_conc,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topleft", legend=c("MC4-Ace-T2.5","MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c"), bty='n')
}
# MC1 vs MC5
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T2.5$Lueders_BD, MC5_T2.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC5_T2.5$Lueders_BD, MC5_T2.5$Ribo_conc,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T3.5$Lueders_BD, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T3.5$Lueders_BD, MC5_T3.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T4.5$Lueders_BD, MC5_T4.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topleft", legend=c("MC1-C12-T4.5", "MC5-Glu-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1))
lines(MC5_T4.5$Lueders_BD, MC5_T4.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topleft", legend=c("MC1-C12-T4.5", "MC5-Glu-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC5_T2.5$Lueders_BD, MC5_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#af953c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#af953c")
lines(MC5_T3.5$Lueders_BD, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
lines(MC5_T4.5$Lueders_BD, MC5_T4.5$Ribo_RMAX,type="o", pch=23, bg="#af953c",
col="#af953c")
legend("topleft", legend=c("MC5-Glu-T2.5","MC5-Glu-T3.5", "MC5-Glu-T4.5"), pch=c(21,22,23),
pt.bg=c("#af953c", "#af953c"), bty='n')
plot(MC5_T2.5$Lueders_BD, MC5_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#af953c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,2.5), col="#af953c")
lines(MC5_T3.5$Lueders_BD, MC5_T3.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
lines(MC5_T4.5$Lueders_BD, MC5_T4.5$Ribo_conc,type="o", pch=23, bg="#af953c",
col="#af953c")
legend("topleft", legend=c("MC5-Glu-T2.5","MC5-Glu-T3.5", "MC5-Glu-T4.5"), pch=c(21,22,23),
pt.bg=c("#af953c", "#af953c"), bty='n')
}
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T2.5$Lueders_BD, MC6_T2.5$Ribo_RMAX,type="o", pch=21, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T2.5$Lueders_BD, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC6_T2.5$Lueders_BD, MC6_T2.5$Ribo_conc,type="o", pch=21, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T3.5$Lueders_BD, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T3.5$Lueders_BD, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T3.5$Lueders_BD, MC6_T3.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T4.5$Lueders_BD, MC6_T4.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topleft", legend=c("MC1-C12-T4.5", "MC6-Xyl-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T4.5$Lueders_BD, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1.5))
lines(MC6_T4.5$Lueders_BD, MC6_T4.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topleft", legend=c("MC1-C12-T4.5", "MC6-Xyl-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC6_T2.5$Lueders_BD, MC6_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders",
ylab="Normalized RNA Conc.", bg='#ba4a4f',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#ba4a4f")
lines(MC6_T3.5$Lueders_BD, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
lines(MC6_T4.5$Lueders_BD, MC6_T4.5$Ribo_RMAX,type="o", pch=23, bg="#ba4a4f",
col="#ba4a4f")
legend("topleft", legend=c("MC6-Xyl-T2.5","MC6-Xyl-T3.5", "MC6-Xyl-T4.5"), pch=c(21,22,23),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n')
plot(MC6_T2.5$Lueders_BD, MC6_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Lueders",
ylab="RNA Conc. (ng/uL)", bg='#ba4a4f',pch=21, xlim=c(1.76,1.86),
ylim=c(0,2.5), col="#ba4a4f")
lines(MC6_T3.5$Lueders_BD, MC6_T3.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
lines(MC6_T4.5$Lueders_BD, MC6_T4.5$Ribo_conc,type="o", pch=23, bg="#ba4a4f",
col="#ba4a4f")
legend("topleft", legend=c("MC6-Xyl-T2.5","MC6-Xyl-T3.5", "MC6-Xyl-T4.5"), pch=c(21,22,23),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n')
}
par(mfrow=c(1,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", pch=22, bg="gray70")
lines(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", bg='gray70',pch=23)
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg=c("gray70", "gray70"), bty='n', cex=1)
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,3.75))
lines(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", pch=22, bg="gray70")
lines(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", bg='gray70',pch=23)
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg=c("gray70", "gray70"), bty='n', cex=1)
#### MC1-C12- vs. MC2-Met
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T2.5$Buckley, MC2_T2.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,3.2))
lines(MC2_T2.5$Buckley, MC2_T2.5$Ribo_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,4.6))
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC2_T2.5$Buckley, MC2_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#a44f9a',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#a44f9a")
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC2-Met-T2.5","MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a"), bty='n')
plot(MC2_T2.5$Buckley, MC2_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#a44f9a',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#a44f9a")
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_conc,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_conc,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC2-Met-T2.5","MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a"), bty='n')
}
# MC1-T2.5 and MC3-Eth-T2.5
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T2.5$Buckley, MC3_T2.5$Ribo_RMAX,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC3_T2.5$Buckley, MC3_T2.5$Ribo_conc,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1.2))
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC3_T2.5$Buckley, MC3_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#6870c8',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#6870c8")
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_RMAX,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC3-Eth-T2.5","MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8"), bty='n')
plot(MC3_T2.5$Buckley, MC3_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#6870c8',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#6870c8")
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_conc,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC3-Eth-T2.5","MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8"), bty='n')
}
######
# MC1 - T2.5 vs. MC4 - Ace
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T2.5$Buckley, MC4_T2.5$Ribo_RMAX,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC4_T2.5$Buckley, MC4_T2.5$Ribo_conc,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,0.7))
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC4_T2.5$Buckley, MC4_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#56ae6c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#56ae6c")
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_RMAX,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC4-Ace-T2.5","MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c"), bty='n')
plot(MC4_T2.5$Buckley, MC4_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#56ae6c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,5), col="#56ae6c")
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_conc,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC4-Ace-T2.5","MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c"), bty='n')
}
# MC1 vs MC5
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T2.5$Buckley, MC5_T2.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC5_T2.5$Buckley, MC5_T2.5$Ribo_conc,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC5_T4.5$Buckley, MC5_T4.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T4.5", "MC5-Glu-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1))
lines(MC5_T4.5$Buckley, MC5_T4.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T4.5", "MC5-Glu-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#af953c"), bty='n')
plot(MC5_T2.5$Buckley, MC5_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#af953c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#af953c")
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
lines(MC5_T4.5$Buckley, MC5_T4.5$Ribo_RMAX,type="o", pch=23, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC5-Glu-T2.5","MC5-Glu-T3.5", "MC5-Glu-T4.5"), pch=c(21,22,23),
pt.bg=c("#af953c", "#af953c"), bty='n')
plot(MC5_T2.5$Buckley, MC5_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#af953c',pch=21, xlim=c(1.76,1.86),
ylim=c(0,2.5), col="#af953c")
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
lines(MC5_T4.5$Buckley, MC5_T4.5$Ribo_conc,type="o", pch=23, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC5-Glu-T2.5","MC5-Glu-T3.5", "MC5-Glu-T4.5"), pch=c(21,22,23),
pt.bg=c("#af953c", "#af953c"), bty='n')
}
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T2.5$Buckley, MC6_T2.5$Ribo_RMAX,type="o", pch=21, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86), ylim=c(0,2.5))
lines(MC6_T2.5$Buckley, MC6_T2.5$Ribo_conc,type="o", pch=21, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.86))
lines(MC6_T4.5$Buckley, MC6_T4.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T4.5", "MC6-Xyl-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1.5))
lines(MC6_T4.5$Buckley, MC6_T4.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T4.5", "MC6-Xyl-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n')
plot(MC6_T2.5$Buckley, MC6_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#ba4a4f',pch=21, xlim=c(1.76,1.86),
ylim=c(0,1), col="#ba4a4f")
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
lines(MC6_T4.5$Buckley, MC6_T4.5$Ribo_RMAX,type="o", pch=23, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC6-Xyl-T2.5","MC6-Xyl-T3.5", "MC6-Xyl-T4.5"), pch=c(21,22,23),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n')
plot(MC6_T2.5$Buckley, MC6_T2.5$Ribo_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='#ba4a4f',pch=21, xlim=c(1.76,1.86),
ylim=c(0,2.5), col="#ba4a4f")
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
lines(MC6_T4.5$Buckley, MC6_T4.5$Ribo_conc,type="o", pch=23, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC6-Xyl-T2.5","MC6-Xyl-T3.5", "MC6-Xyl-T4.5"), pch=c(21,22,23),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n')
}
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP == "4.5")
MC1_T2.5=subset(read, read$MC=="MC1" & TP == "2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP == "3.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc. (ribogreen)", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T2.5$Corrected, MC2_T2.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T2.5$Buckley, MC2_T2.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T3.5$Corrected, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Corrected, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc. ", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T4.5$Corrected, MC2_T4.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC2_T2.5$Corrected, MC2_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#a44f9a',pch=21, xlim=c(1.735,1.85),
col="#a44f9a")
lines(MC2_T3.5$Corrected, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Corrected, MC2_T4.5$Ribo_RMAX,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC2-Met-T2.5", "MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a","#a44f9a"), bty='n')
plot(MC2_T2.5$Buckley, MC2_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#a44f9a',pch=21, xlim=c(1.735,1.85),
col="#a44f9a")
lines(MC2_T3.5$Buckley, MC2_T3.5$Ribo_RMAX,type="o", pch=22, bg="#a44f9a",
col="#a44f9a")
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=23, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC2-Met-T2.5", "MC2-Met-T3.5", "MC2-Met-T4.5"), pch=c(21,22,23),
pt.bg=c("#a44f9a", "#a44f9a","#a44f9a"), bty='n')
}
# MC1-T2.5 and MC3-Eth-T2.5
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP == "4.5")
MC1_T2.5=subset(read, read$MC=="MC1" & TP == "2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP == "3.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T2.5$Corrected, MC3_T2.5$Ribo_RMAX,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T2.5$Buckley, MC3_T2.5$Ribo_RMAX,type="o", pch=21, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T3.5$Corrected, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Corrected, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T4.5$Corrected, MC3_T4.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T4.5", "MC3-Eth-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#6870c8"), bty='n')
plot(MC3_T2.5$Corrected, MC3_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#6870c8',pch=21, xlim=c(1.735,1.85),
col="#6870c8")
lines(MC3_T3.5$Corrected, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Corrected, MC3_T4.5$Ribo_RMAX,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC3-Eth-T2.5", "MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8","#6870c8"), bty='n')
plot(MC3_T2.5$Buckley, MC3_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc. ", bg='#6870c8',pch=21, xlim=c(1.735,1.85),
col="#6870c8")
lines(MC3_T3.5$Buckley, MC3_T3.5$Ribo_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
lines(MC3_T4.5$Buckley, MC3_T4.5$Ribo_RMAX,type="o", pch=23, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC3-Eth-T2.5", "MC3-Eth-T3.5", "MC3-Eth-T4.5"), pch=c(21,22,23),
pt.bg=c("#6870c8", "#6870c8","#6870c8"), bty='n')
}
######
# MC1 - T2.5 vs. MC4 - Ace
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(4,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T2.5$Corrected, MC4_T2.5$Ribo_RMAX,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T2.5$Buckley, MC4_T2.5$Ribo_RMAX,type="o", pch=21, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T3.5$Corrected, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Corrected, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T4.5$Corrected, MC4_T4.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.74,1.84))
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T4.5", "MC4-Ace-T4.5"), pch=c(21,22),
pt.bg=c("gray70", "#56ae6c"), bty='n')
plot(MC4_T2.5$Corrected, MC4_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#56ae6c',pch=21, xlim=c(1.74,1.84),
col="#56ae6c")
lines(MC4_T3.5$Corrected, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Corrected, MC4_T4.5$Ribo_RMAX,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC4-Ace-T2.5", "MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c","#56ae6c"), bty='n')
plot(MC4_T2.5$Buckley, MC4_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#56ae6c',pch=21, xlim=c(1.74,1.84),
col="#56ae6c")
lines(MC4_T3.5$Buckley, MC4_T3.5$Ribo_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
lines(MC4_T4.5$Buckley, MC4_T4.5$Ribo_RMAX,type="o", pch=23, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC4-Ace-T2.5", "MC4-Ace-T3.5", "MC4-Ace-T4.5"), pch=c(21,22,23),
pt.bg=c("#56ae6c", "#56ae6c","#56ae6c"), bty='n')
}
# MC1 vs MC5
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(3,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC5_T2.5$Corrected, MC5_T2.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC5_T2.5$Buckley, MC5_T2.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC5_T3.5$Corrected, MC5_T3.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_RMAX,type="o", pch=21, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC5_T2.5$Corrected, MC5_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#af953c',pch=21, xlim=c(1.7, 1.83),
col="#af953c")
lines(MC5_T3.5$Corrected, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC5-Glu-T2.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("#af953c", "#af953c"), bty='n', cex=0.9)
plot(MC5_T2.5$Buckley, MC5_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#af953c',pch=21, xlim=c(1.7, 1.83),
col="#af953c")
lines(MC5_T3.5$Buckley, MC5_T3.5$Ribo_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC5-Glu-T2.5", "MC5-Glu-T3.5"), pch=c(21,22),
pt.bg=c("#af953c", "#af953c"), bty='n', cex=0.9)
}
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mar=c(5,5,1,1),mfrow=c(3,2))
plot(MC1_T2.5$Corrected, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC6_T2.5$Corrected, MC6_T2.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.83))
lines(MC6_T2.5$Buckley, MC6_T2.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.7, 1.84))
lines(MC6_T3.5$Corrected, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.75, 1.85))
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC6_T2.5$Corrected, MC6_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='#ba4a4f',pch=21, xlim=c(1.7, 1.84),
col="#ba4a4f")
lines(MC6_T3.5$Corrected, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC6-Xyl-T2.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n', cex=0.9)
plot(MC6_T2.5$Buckley, MC6_T2.5$Ribo_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='#ba4a4f',pch=21, xlim=c(1.75, 1.85),
col="#ba4a4f")
lines(MC6_T3.5$Buckley, MC6_T3.5$Ribo_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC6-Xyl-T2.5", "MC6-Xyl-T3.5"), pch=c(21,22),
pt.bg=c("#ba4a4f", "#ba4a4f"), bty='n', cex=0.9)
}
{
par(mar=c(5,5,1,1))
plot(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", xlab="Buoyant Density (g/mL)",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.76,1.84), ylim=c(0,1),
yaxt='n',xaxt='n', cex.lab=1.2, bty='n',cex=1.4)
rect(xleft=1.787, xright=1.794, ybottom=0, ytop=1.03, col= rgb(0.9960784,0.9411765,0.2745098,alpha=0.8),lty=1, lwd=0)
#rect(xleft=1.807990115-0.0035, xright=1.807990115+0.0035, ybottom=0, ytop=1.03, col= rgb(0.5529412,0.08627451,0.08627451,alpha=0.7),lty=1, lwd=0)
rect(xleft=1.807990115-0.0035, xright=1.807990115+0.0035, ybottom=0, ytop=1.03, col= rgb(0.9058824,0.1803922,0.1803922,alpha=0.3),lty=1, lwd=0)
lines(MC1_T4.5$Buckley, MC1_T4.5$Ribo_RMAX,type="o", pch=21, bg="gray70",cex=1.4)
axis(1,at=c(1.76,1.78,1.80,1.82,1.84), lwd=1)
axis(2,at=c(0,0.25,0.5,0.75,1),lwd=1)
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="black",cex=1.4)
lines(MC2_T4.5$Buckley, MC2_T4.5$Ribo_RMAX,type="o", pch=21, bg="#a44f9a",
col="black",cex=1.4)
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
}
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected", xlim=c(1.7, 1.83),
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", pch=22, bg="gray70",
col="black")
lines(MC1_T4.5$Corrected, MC1_T4.5$qPCR_RMAX,type="o", pch=23, bg="gray70",
col="black")
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5", "MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg="gray70", bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley", xlim=c(1.73, 1.85),
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", pch=22, bg="gray70",
col="black")
lines(MC1_T4.5$Buckley, MC1_T4.5$qPCR_RMAX,type="o", pch=23, bg="gray70",
col="black")
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T3.5"), pch=c(21,22,23),
pt.bg="gray70", bty='n')
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected", xlim=c(1.7, 1.83),ylim=c(0,20),
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", pch=22, bg="gray70",
col="black")
lines(MC1_T4.5$Corrected, MC1_T4.5$qPCR_conc,type="o", pch=23, bg="gray70",
col="black")
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5", "MC1-C12-T4.5"), pch=c(21,22,23),
pt.bg="gray70", bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley", xlim=c(1.73, 1.85),
ylim=c(0,20),
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", pch=22, bg="gray70",
col="black")
lines(MC1_T4.5$Buckley, MC1_T4.5$qPCR_conc,type="o", pch=23, bg="gray70",
col="black")
legend("topright", legend=c("MC1-C12-T2.5", "MC1-C12-T3.5","MC1-C12-T3.5"), pch=c(21,22,23),
pt.bg="gray70", bty='n')
}
#### T2.5
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_30Aug22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP == "4.5")
MC1_T2.5=subset(read, read$MC=="MC1" & TP == "2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP == "3.5")
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T2.5$Corrected, MC2_T2.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC2_T2.5$Buckley, MC2_T2.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0.00001,20))
lines(MC2_T2.5$Corrected, MC2_T2.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0.00001,20))
lines(MC2_T2.5$Buckley, MC2_T2.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T2.5", "MC2-Met-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
}
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T2.5$Corrected, MC3_T2.5$qPCR_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC3_T2.5$Buckley, MC3_T2.5$qPCR_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0,25))
lines(MC3_T2.5$Corrected, MC3_T2.5$qPCR_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0,25))
lines(MC3_T2.5$Buckley, MC3_T2.5$qPCR_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T2.5", "MC3-Eth-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
}
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC4_T2.5$Corrected, MC4_T2.5$qPCR_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC4_T2.5$Buckley, MC4_T2.5$qPCR_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC4_T2.5$Corrected, MC4_T2.5$qPCR_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC4_T2.5$Buckley, MC4_T2.5$qPCR_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T2.5", "MC4-Ace-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
}
REDO SPIN
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC5_T2.5$Corrected, MC5_T2.5$qPCR_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC5_T2.5$Buckley, MC5_T2.5$qPCR_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0,7.25))
lines(MC5_T2.5$Corrected, MC5_T2.5$qPCR_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0,7.25))
lines(MC5_T2.5$Buckley, MC5_T2.5$qPCR_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T2.5", "MC5-Glu-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
}
REDO SPIN
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC6_T2.5$Corrected, MC6_T2.5$qPCR_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85))
lines(MC6_T2.5$Buckley, MC6_T2.5$qPCR_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T2.5$Corrected, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0, 40))
lines(MC6_T2.5$Corrected, MC6_T2.5$qPCR_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T2.5$Buckley, MC1_T2.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21, xlim=c(1.735,1.85),
ylim=c(0, 40))
lines(MC6_T2.5$Buckley, MC6_T2.5$qPCR_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T2.5", "MC6-Xyl-T2.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
}
read=read.csv('/Users/oliviaahern/Documents/R/Exp4/25Aug22/qpcr_1Sept22.csv',header=T)
MC2_T2.5=subset(read, read$MC=="MC2" & TP =="2.5")
MC2_T3.5=subset(read, read$MC=="MC2" & TP =="3.5")
MC2_T4.5=subset(read, read$MC=="MC2" & TP =="4.5")
MC1_T4.5=subset(read, read$MC=="MC1" & TP == "4.5")
MC1_T2.5=subset(read, read$MC=="MC1" & TP == "2.5")
MC1_T3.5=subset(read, read$MC=="MC1" & TP == "3.5")
MC3_T2.5=subset(read, read$MC=="MC3" & TP =="2.5")
MC3_T3.5=subset(read, read$MC=="MC3" & TP =="3.5")
MC3_T4.5=subset(read, read$MC=="MC3" & TP =="4.5")
MC4_T2.5=subset(read, read$MC=="MC4" & TP =="2.5")
MC4_T3.5=subset(read, read$MC=="MC4" & TP =="3.5")
MC4_T4.5=subset(read, read$MC=="MC4" & TP =="4.5")
MC5_T2.5=subset(read, read$MC=="MC5" & TP =="2.5")
MC5_T3.5=subset(read, read$MC=="MC5" & TP =="3.5")
MC5_T4.5=subset(read, read$MC=="MC5" & TP =="4.5")
MC6_T2.5=subset(read, read$MC=="MC6" & TP =="2.5")
MC6_T3.5=subset(read, read$MC=="MC6" & TP =="3.5")
MC6_T4.5=subset(read, read$MC=="MC6" & TP =="4.5")
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC2_T3.5$Corrected, MC2_T3.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC2_T3.5$Buckley, MC2_T3.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0.00001,20))
lines(MC2_T3.5$Corrected, MC2_T3.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0.00001,20))
lines(MC2_T3.5$Buckley, MC2_T3.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T3.5", "MC2-Met-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
}
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC3_T3.5$Corrected, MC3_T3.5$qPCR_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC3_T3.5$Buckley, MC3_T3.5$qPCR_RMAX,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0,20))
lines(MC3_T3.5$Corrected, MC3_T3.5$qPCR_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0,20))
lines(MC3_T3.5$Buckley, MC3_T3.5$qPCR_conc,type="o", pch=22, bg="#6870c8",
col="#6870c8")
legend("topright", legend=c("MC1-C12-T3.5", "MC3-Eth-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#6870c8"), bty='n', cex=0.9)
}
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC4_T3.5$Corrected, MC4_T3.5$qPCR_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC4_T3.5$Buckley, MC4_T3.5$qPCR_RMAX,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC4_T3.5$Corrected, MC4_T3.5$qPCR_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC4_T3.5$Buckley, MC4_T3.5$qPCR_conc,type="o", pch=22, bg="#56ae6c",
col="#56ae6c")
legend("topright", legend=c("MC1-C12-T3.5", "MC4-Ace-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#56ae6c"), bty='n', cex=0.9)
}
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC5_T3.5$Corrected, MC5_T3.5$qPCR_RMAX,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC5_T3.5$Buckley, MC5_T3.5$qPCR_RMAX,type="o", pch=22, bg="#af953c", col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC5_T3.5$Corrected, MC5_T3.5$qPCR_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21)
lines(MC5_T3.5$Buckley, MC5_T3.5$qPCR_conc,type="o", pch=22, bg="#af953c",
col="#af953c")
legend("topright", legend=c("MC1-C12-T3.5", "MC5-Glu-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#af953c"), bty='n', cex=0.9)
}
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC6_T3.5$Corrected, MC6_T3.5$qPCR_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC6_T3.5$Buckley, MC6_T3.5$qPCR_RMAX,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Corrected, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC6_T3.5$Corrected, MC6_T3.5$qPCR_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
plot(MC1_T3.5$Buckley, MC1_T3.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc.", bg='gray70',pch=21)
lines(MC6_T3.5$Buckley, MC6_T3.5$qPCR_conc,type="o", pch=22, bg="#ba4a4f",
col="#ba4a4f")
legend("topright", legend=c("MC1-C12-T3.5", "MC6-Xyl-T3.5"), pch=c(21,21),
pt.bg=c("gray70", "#ba4a4f"), bty='n', cex=0.9)
}
{
par(mfrow=c(2,2), mar=c(5,5,1,1))
plot(MC1_T4.5$Corrected, MC1_T4.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC2_T4.5$Corrected, MC2_T4.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$qPCR_RMAX,type="o", xlab="Buoyant Density - Buckley",
ylab="Normalized RNA Conc", bg='gray70',pch=21)
lines(MC2_T4.5$Buckley, MC2_T4.5$qPCR_RMAX,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Corrected, MC1_T4.5$qPCR_conc,type="o", xlab="Buoyant Density - Lueders Corrected",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0.00001,10))
lines(MC2_T4.5$Corrected, MC2_T4.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
plot(MC1_T4.5$Buckley, MC1_T4.5$qPCR_conc,type="o", xlab="Buoyant Density - Buckley",
ylab="RNA Conc. (ng/uL)", bg='gray70',pch=21,
ylim=c(0.00001,10))
lines(MC2_T4.5$Buckley, MC2_T4.5$qPCR_conc,type="o", pch=21, bg="#a44f9a",
col="#a44f9a")
legend("topright", legend=c("MC1-C12-T4.5", "MC2-Met-T4.5"), pch=c(21,21),
pt.bg=c("gray70", "#a44f9a"), bty='n')
}
library(phyloseq)
x<-read.csv(file='/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/Sequences/asv-table.csv',header=TRUE,row.names=1)
OTU = otu_table(x, taxa_are_rows=T)
taxa<-read.csv(file="/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/Sequences/taxonomy.csv",header=TRUE,row.names=1)
t<-as.matrix(taxa)
tax2<-tax_table(t)
map<-import_qiime_sample_data("/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/Sequences/map_exp4.txt")
tree=read.tree('/Users/oliviaahern/Documents/MBL_WHOI/Trophic_Cascades/Experiment4/Sequences/tree.nwk')
phyo = phyloseq(OTU, tax2,map,tree)
phyo
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 2102 taxa and 96 samples ]
## sample_data() Sample Data: [ 96 samples by 8 sample variables ]
## tax_table() Taxonomy Table: [ 2102 taxa by 8 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 2102 tips and 2100 internal nodes ]
phyo1 = subset_taxa(phyo, !Order=="Chloroplast")
phyo2 = subset_taxa(phyo1, !Family=="Mitochondria")
phyo=phyo2
phyo
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 1921 taxa and 96 samples ]
## sample_data() Sample Data: [ 96 samples by 8 sample variables ]
## tax_table() Taxonomy Table: [ 1921 taxa by 8 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 1921 tips and 1919 internal nodes ]
phyo_abund=transform_sample_counts(phyo, function(x) (x/sum(x)))
pd <- psmelt(phyo_abund)
colors=readRDS('/Users/oliviaahern/Documents/GitHub/Exp4/colors_asvs.rds')
library(grid)
#palette(as.character(t(colors)))
d_rgn = ggplot(pd, aes(x = reorder(Sample, Timepoint), y = Abundance, fill = Strain)) +
scale_fill_manual(values=as.character(t(colors))) +
geom_bar(stat = "identity", width=0.97, color='black',
lwd=0.1) +
facet_grid(~MC, scale='free_x', space="free", shrink=TRUE) +
labs(x=" ", y = "ASV Relative Abundance") +
theme_bw() +
theme(axis.text = element_text(color ='black',size=12, hjust=1,vjust=1),
axis.text.x=element_text(size=8, angle=90),
axis.title = element_text(color='black',face='bold',size=14),
legend.position = "none",
panel.grid=element_blank(),
strip.text.x = element_text(
size = 10, color = "black", face = "bold"),
strip.background = element_rect(
color="white", fill="white", size=1, linetype="solid"),
panel.spacing = unit(0.05, "lines"))
d_rgn
Under construction
phyo_nop=subset_samples(phyo, B_C!='pond')
library(plyr)
# get abundance in %
phy <- transform_sample_counts(phyo_nop, function(x) x/sum(x))
# create dataframe from phyloseq object
dat <- psmelt(phy)
# convert Phylum to a character vector from a factor because R
dat$OTU <- as.character(dat$OTU)
# group dataframe by Phylum, calculate median rel. abundance
medians <- ddply(dat, ~OTU, function(x) c(median=median(x$Abundance)))
# find Phyla whose rel. abund. is less than 0.1%
remainder <- medians[medians$median <= 0.00001,]$OTU
# change their name to "Other"
dat[dat$OTU %in% remainder,]$OTU <- 'Other <0.1%'
# boxplot
blah=data.frame(tax_table(phyo_abund))
nan=cbind(row.names(blah), (colors))
nano = data.frame(nan)
colnames(nano) = c("OTU", "Colors")
subs=levels(as.factor(dat$OTU))
sub=subset(nano, OTU %in% subs)
color2=c(sub$Colors, 'gray80')
p_rgn = ggplot(dat, aes(x = reorder(Sample, Timepoint), y = Abundance, fill = OTU)) +
scale_fill_manual(values=as.character(t((color2)))) +
geom_bar(stat = "identity", width=0.97, color='black',
lwd=0.1) +
facet_grid(~MC, scale='free_x', space="free", shrink=TRUE) +
labs(x=" ", y = "ASV Relative Abundance") +
theme_bw() +
theme(axis.text = element_text(color ='black',size=12, hjust=1,vjust=1),
axis.text.x=element_text(size=8, angle=90),
axis.title = element_text(color='black',face='bold',size=14),
legend.position = "bottom",
panel.grid=element_blank(),
legend.text = element_text(size=6),
legend.key.size = unit(0.25,'cm'),
#strip.text.x = element_text(
# size = 10, color = "black", face = "bold"),
#strip.background = element_rect(
# color="white", fill="white", size=1, linetype="solid"),
#panel.spacing = unit(0.05, "lines")
)
p_rgn
#library(plotly)
#fig <- ggplotly(p_rgn)
#fig
Working on this plot
phyo_nop_g=tax_glom(phyo_nop, taxrank="Genus")
library(plyr)
# get abundance in %
phy <- transform_sample_counts(phyo_nop_g, function(x) x/sum(x))
# create dataframe from phyloseq object
dat <- psmelt(phy)
# convert Phylum to a character vector from a factor because R
dat$Genus <- as.character(dat$Genus)
dat$Genus[dat$Genus==""] <- NA
# group dataframe by Phylum, calculate median rel. abundance
medians <- ddply(dat, ~Genus, function(x) c(median=median(x$Abundance)))
# find Phyla whose rel. abund. is less than 0.1%
remainder <- medians[medians$median <= 0.00001,]$Genus
# change their name to "Other"
dat[dat$Genus %in% remainder,]$Genus <- 'Other <0.1%'
# boxplot
blah=data.frame(tax_table(phyo_abund))
nan=cbind(blah$Genus, (colors))
nano = data.frame(nan)
colnames(nano) = c("Genus", "Colors")
subs=levels(as.factor(dat$Genus))
sub=subset(nano, Genus %in% subs)
color4=c(sub$Colors, 'gray80')
p_rgn = ggplot(dat, aes(x = reorder(Sample, Timepoint), y = Abundance, fill = Genus)) +
scale_fill_manual(values=as.character(t((color4)))) +
geom_bar(stat = "identity", width=0.97, color='black',
lwd=0.1) +
facet_grid(~MC, scale='free_x', space="free", shrink=TRUE) +
labs(x=" ", y = "Genus Relative Abundance") +
theme_bw() +
theme(axis.text = element_text(color ='black',size=12, hjust=1,vjust=1),
axis.text.x=element_text(size=8, angle=90),
axis.title = element_text(color='black',face='bold',size=14),
legend.position = "bottom",
panel.grid=element_blank(),
legend.text = element_text(size=6),
legend.key.size = unit(0.25, 'cm')
#strip.text.x = element_text(
# size = 10, color = "black", face = "bold"),
#strip.background = element_rect(
# color="white", fill="white", size=1, linetype="solid"),
#panel.spacing = unit(0.05, "lines")
)
p_rgn
#library(plotly)
#fig <- ggplotly(p_rgn)
#fig
micro=microbiome::aggregate_taxa(phyo, "Class")
phyo_abund=transform_sample_counts(micro, function(x) (x/sum(x)))
pd <- psmelt(phyo_abund)
colors=readRDS("/Users/oliviaahern/Documents/GitHub/Exp4/c_class.rds")
library(grid)
#palette(as.character(t(colors)))
d_rgn = ggplot(pd, aes(x = reorder(Sample, Timepoint), y = Abundance, fill = Class)) +
scale_fill_manual(values=as.character(t(colors))) +
geom_bar(stat = "identity", width=0.97, color='black',
lwd=0.1) +
facet_grid(~MC, scale='free_x', space="free", shrink=TRUE) +
labs(x=" ", y = "Class Relative Abundance") +
theme_bw() +
theme(axis.text = element_text(color ='black',size=12, hjust=1,vjust=1),
axis.text.x=element_text(size=8, angle=90),
axis.title = element_text(color='black',face='bold',size=14),
legend.position = "bottom",
panel.grid=element_blank(),
strip.text.x = element_text(
size = 10, color = "black", face = "bold"),
legend.text = element_text(size=6),
legend.key.size = unit(0.25, 'cm')
#strip.background = element_rect(
# color="white", fill="white", size=1, linetype="solid"),
# panel.spacing = unit(0.05, "lines"))
)
d_rgn
Euclidean distance of centered log ratio transformed data
Transform data - remove ASVs that are less than 0.01% of total dataset and minimum reads of 2. Aitchinson’s distance - Euclidean distance of centered log ratio data.
library(CoDaSeq)
library(compositions)
input=t(data.frame(otu_table(phyo)))
dim(input)
## [1] 96 1921
d.subset <- codaSeq.filter(input,
samples.by.row=T,min.reads=2,min.prop =0.0001)
dim(d.subset)
## [1] 1145 96
log_rats <- (compositions::clr(t(d.subset)))
OTU=otu_table(t(log_rats),taxa_are_rows = T)
comp_clr=phyloseq(OTU,map,tax2)
otu=t(otu_table(comp_clr))
euc=vegdist(otu,'euc')
p=prcomp(euc)
# summary(p)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(comp_clr)$pch,
bg=sample_data(comp_clr)$col,cex.lab=1.3,
xlab= 'PCoA1 62.10%', ylab='PCoA2 13.71%',cex=1.5)
legend(60,60, legend=c("MC1-C12 Batch","MC1-C12 Chemostat",
"MC2-Met Batch", "MC2-Met Chemostat",
"MC3-Eth Batch", "MC3-Eth Chemostat",
"MC4-Ace Batch", "MC4-Ace Chemostat",
"MC5-Glu Batch", "MC5-Glu Chemostat",
"MC6-Xyl Batch", "MC6-Xyl Chemostat",
"Pond"),xpd=T,
pt.bg=c("gray70","gray70","#a44f9a","#a44f9a","#6870c8","#6870c8",
"#56ae6c","#56ae6c","#af953c","#af953c","#ba4a4f","#ba4a4f",
"black"),
pch=c(21,23,21,23,21,23,21,23,21,23,21,23, 24),
bty='n',cex=1)
ordiellipse(p, groups=sample_data(comp_clr)$Timepoint)
}
Transform data - remove ASVs that are less than 0.01% of total dataset and minimum reads of 2. Aitchinson’s distance - Euclidean distance of centered log ratio data.
data1=subset_samples(phyo, Treatment !="Pond")
input=t(data.frame(otu_table(data1)))
dim(input)
## [1] 94 1921
d.subset <- codaSeq.filter(input,
samples.by.row=T,min.reads=2,min.prop =0.0001)
dim(d.subset)
## [1] 748 94
log_rats <- (compositions::clr(t(d.subset)))
OTU=otu_table(t(log_rats),taxa_are_rows = T)
comp_clr=phyloseq(OTU,map,tax2)
otu=t(otu_table(comp_clr))
euc=vegdist(otu,'euc')
p=prcomp(otu)
#summary(p)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(data1)$pch,
bg=sample_data(data1)$col,cex.lab=1.3,
xlab= 'PCoA1 29.17%', ylab='PCoA2 11.24%',cex=1.5)
legend(12,20, legend=c("MC1-C12 Batch","MC1-C12 Chemostat",
"MC2-Met Batch", "MC2-Met Chemostat",
"MC3-Eth Batch", "MC3-Eth Chemostat",
"MC4-Ace Batch", "MC4-Ace Chemostat",
"MC5-Glu Batch", "MC5-Glu Chemostat",
"MC6-Xyl Batch", "MC6-Xyl Chemostat"),xpd=T,
pt.bg=c("gray70","gray70","#a44f9a","#a44f9a","#6870c8","#6870c8",
"#56ae6c","#56ae6c","#af953c","#af953c","#ba4a4f","#ba4a4f"),
pch=c(21,23,21,23,21,23,21,23,21,23,21,23),
bty='n',cex=1)
ordiellipse(p, groups=sample_data(comp_clr)$Timepoint)
}
Ellipses represent 80% confidence intervals around the centroid of the Timepoint.
Data is significantly tied to the timepoint sampled (adonis2, R2=0.23, F=9.4, p<0.001) not the Treatment/MC (adonis2, R2=0.08, F=0.7, p=0.973).
data1=subset_samples(comp_clr, B_C =="Batch")
otu=t(otu_table(data1))
euc=vegdist(otu,'euc')
p=prcomp(otu)
#summary(p)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(data1)$pch,
bg=sample_data(data1)$col,cex.lab=1.3,
xlab= 'PCoA1 31.54%', ylab='PCoA2 14.79%',cex=1.5)
ordiellipse(p, groups=sample_data(data1)$Timepoint,
label=FALSE)
legend(12,5, legend=c("MC1-C12 Batch",
"MC2-Met Batch",
"MC3-Eth Batch",
"MC4-Ace Batch",
"MC5-Glu Batch",
"MC6-Xyl Batch"),xpd=T,
pt.bg=c("gray70","#a44f9a","#6870c8",
"#56ae6c","#af953c","#ba4a4f"),
pch=21,
bty='n',cex=1)
}
adonis2(euc~sample_data(data1)$Timepoint + sample_data(data1)$Treatment,
by='margin')
## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = euc ~ sample_data(data1)$Timepoint + sample_data(data1)$Treatment, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(data1)$Timepoint 1 2581.6 0.22551 9.3967 0.001 ***
## sample_data(data1)$Treatment 5 899.0 0.07853 0.6544 0.965
## Residual 29 7967.4 0.69596
## Total 35 11448.0 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Ellipses represent 80% confidence intervals around the centroid of the Treatment.
Chemostat data is significantly associated with both Timepoint (adonis2, R2=0.06, F=5.5, p<0.001) and Treatment/MC (adonis2, R2=0.39, F=6.8, p<0.001).
data1=subset_samples(comp_clr, B_C =="Chemostat")
otu=t(otu_table(data1))
euc=vegdist(otu,'euc')
p=prcomp(otu)
#summary(p)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(data1)$pch,
bg=sample_data(data1)$col,cex.lab=1.3,
xlab= 'PCoA1 17.66%', ylab='PCoA2 12.52%',cex=1.5)
ordiellipse(p, groups=sample_data(data1)$Treatment,label=TRUE)
legend(15.5,5, legend=c("MC1-C12 Chemostat",
"MC2-Met Chemostat",
"MC3-Eth Chemostat",
"MC4-Ace Chemostat",
"MC5-Glu Chemostat",
"MC6-Xyl Chemostat"),xpd=T,
pt.bg=c("gray70","#a44f9a","#6870c8",
"#56ae6c","#af953c","#ba4a4f"),
pch=23,
bty='n',cex=1)
}
adonis2(euc~sample_data(data1)$Timepoint + sample_data(data1)$Treatment,
by='margin')
## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = euc ~ sample_data(data1)$Timepoint + sample_data(data1)$Treatment, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(data1)$Timepoint 1 679.1 0.06347 5.5055 0.001 ***
## sample_data(data1)$Treatment 5 4222.4 0.39465 6.8461 0.001 ***
## Residual 47 5797.5 0.54187
## Total 53 10699.0 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
library(philr)
GP <- transform_sample_counts(phyo, function(x) x+1)
phy_tree(GP) <- makeNodeLabel(phy_tree(GP), method="number", prefix='n')
name.balance(phy_tree(GP), tax_table(GP), 'n1')
## [1] "Species_/Kingdom_Bacteria"
otu.table <- t(otu_table(GP))
treefr <- phy_tree(GP)
metadata <- sample_data(GP)
tax <- tax_table(GP)
gp.philr <- philr(otu.table, treefr,
part.weights='enorm.x.gm.counts',
ilr.weights='blw.sqrt')
gp.dist <- dist(gp.philr, method="euclidean")
p <- prcomp(gp.dist)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(phyo)$pch,
bg=sample_data(phyo)$col,cex.lab=1.3,
xlab= 'PCoA1 79.27%', ylab='PCoA2 9.19%',cex=1.5)
legend(80,45, legend=c("MC1-C12 Batch","MC1-C12 Chemostat",
"MC2-Met Batch", "MC2-Met Chemostat",
"MC3-Eth Batch", "MC3-Eth Chemostat",
"MC4-Ace Batch", "MC4-Ace Chemostat",
"MC5-Glu Batch", "MC5-Glu Chemostat",
"MC6-Xyl Batch", "MC6-Xyl Chemostat",
"Pond"),xpd=T,
pt.bg=c("gray70","gray70","#a44f9a","#a44f9a","#6870c8","#6870c8",
"#56ae6c","#56ae6c","#af953c","#af953c","#ba4a4f","#ba4a4f",
"black"),
pch=c(21,23,21,23,21,23,21,23,21,23,21,23, 24),
bty='n',cex=1)
}
Samples significantly tied to
phyo1=subset_samples(phyo, B_C !="Pond")
GP <- transform_sample_counts(phyo1, function(x) x+1)
phy_tree(GP) <- makeNodeLabel(phy_tree(GP), method="number", prefix='n')
name.balance(phy_tree(GP), tax_table(GP), 'n1')
## [1] "Species_/Kingdom_Bacteria"
otu.table <- t(otu_table(GP))
treefr <- phy_tree(GP)
metadata <- sample_data(GP)
tax <- tax_table(GP)
gp.philr <- philr(otu.table, treefr,
part.weights='enorm.x.gm.counts',
ilr.weights='blw.sqrt')
gp.dist <- dist(gp.philr, method="euclidean")
p <- prcomp(gp.dist)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(phyo1)$pch,
bg=sample_data(phyo1)$col,cex.lab=1.3,
xlab= 'PCoA1 78.84%', ylab='PCoA2 9.93%',cex=1.5)
legend(80,45, legend=c("MC1-C12 Batch","MC1-C12 Chemostat",
"MC2-Met Batch", "MC2-Met Chemostat",
"MC3-Eth Batch", "MC3-Eth Chemostat",
"MC4-Ace Batch", "MC4-Ace Chemostat",
"MC5-Glu Batch", "MC5-Glu Chemostat",
"MC6-Xyl Batch", "MC6-Xyl Chemostat"),xpd=T,
pt.bg=c("gray70","gray70","#a44f9a","#a44f9a","#6870c8","#6870c8",
"#56ae6c","#56ae6c","#af953c","#af953c","#ba4a4f","#ba4a4f"),
pch=c(21,23,21,23,21,23,21,23,21,23,21,23),
bty='n',cex=1)
}
adonis2(gp.dist~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint + sample_data(phyo1)$B_C, by='margin')
## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = gp.dist ~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint + sample_data(phyo1)$B_C, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(phyo1)$Treatment 5 2060.8 0.12580 6.2597 0.001 ***
## sample_data(phyo1)$Timepoint 1 351.2 0.02144 5.3335 0.005 **
## sample_data(phyo1)$B_C 1 842.8 0.05145 12.7998 0.001 ***
## Residual 82 5399.1 0.32959
## Total 89 16381.4 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Samples significantly tied to
phyo1=subset_samples(phyo, B_C =="Batch")
GP <- transform_sample_counts(phyo1, function(x) x+1)
phy_tree(GP) <- makeNodeLabel(phy_tree(GP), method="number", prefix='n')
name.balance(phy_tree(GP), tax_table(GP), 'n1')
## [1] "Species_/Kingdom_Bacteria"
otu.table <- t(otu_table(GP))
treefr <- phy_tree(GP)
metadata <- sample_data(GP)
tax <- tax_table(GP)
gp.philr <- philr(otu.table, treefr,
part.weights='enorm.x.gm.counts',
ilr.weights='blw.sqrt')
gp.dist <- dist(gp.philr, method="euclidean")
p <- prcomp(gp.dist)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(phyo1)$pch,
bg=sample_data(phyo1)$col,cex.lab=1.3,
xlab= 'PCoA1 64.96%', ylab='PCoA2 18.17%',cex=1.5)
ordiellipse(p, groups=sample_data(phyo1)$Timepoint,
label=TRUE, cex=1.5)
legend(90,20, legend=c("MC1-C12 Batch",
"MC2-Met Batch",
"MC3-Eth Batch",
"MC4-Ace Batch",
"MC5-Glu Batch",
"MC6-Xyl Batch"),xpd=T,
pt.bg=c("gray70","#a44f9a","#6870c8",
"#56ae6c","#af953c","#ba4a4f"),
pch=21,
bty='n',cex=1)
}
adonis2(gp.dist~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint, by='margin')
## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = gp.dist ~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(phyo1)$Treatment 5 818.1 0.04186 0.3267 0.993
## sample_data(phyo1)$Timepoint 1 4202.7 0.21501 8.3907 0.003 **
## Residual 29 14525.5 0.74313
## Total 35 19546.3 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Samples significantly tied to
phyo1=subset_samples(phyo, B_C =="Chemostat")
GP <- transform_sample_counts(phyo1, function(x) x+1)
phy_tree(GP) <- makeNodeLabel(phy_tree(GP), method="number", prefix='n')
name.balance(phy_tree(GP), tax_table(GP), 'n1')
## [1] "Species_/Kingdom_Bacteria"
otu.table <- t(otu_table(GP))
treefr <- phy_tree(GP)
metadata <- sample_data(GP)
tax <- tax_table(GP)
gp.philr <- philr(otu.table, treefr,
part.weights='enorm.x.gm.counts',
ilr.weights='blw.sqrt')
gp.dist <- dist(gp.philr, method="euclidean")
p <- prcomp(gp.dist)
{
par(mar=c(7,8,1,10))
plot(p$x[,1],p$x[,2], pch = sample_data(data1)$pch,
bg=sample_data(data1)$col,cex.lab=1.3,
xlab= 'PCoA1 53.93%', ylab='PCoA2 24.54%',cex=1.5)
ordiellipse(p, groups=sample_data(data1)$Treatment,label=TRUE)
legend(85,50, legend=c("MC1-C12 Chemostat",
"MC2-Met Chemostat",
"MC3-Eth Chemostat",
"MC4-Ace Chemostat",
"MC5-Glu Chemostat",
"MC6-Xyl Chemostat"),xpd=T,
pt.bg=c("gray70","#a44f9a","#6870c8",
"#56ae6c","#af953c","#ba4a4f"),
pch=23,
bty='n',cex=1)
}
adonis2(gp.dist~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint, by='margin')
## Permutation test for adonis under reduced model
## Marginal effects of terms
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = gp.dist ~ sample_data(phyo1)$Treatment + sample_data(phyo1)$Timepoint, by = "margin")
## Df SumOfSqs R2 F Pr(>F)
## sample_data(phyo1)$Treatment 5 12134.8 0.58701 16.814 0.001 ***
## sample_data(phyo1)$Timepoint 1 1753.5 0.08482 12.148 0.001 ***
## Residual 47 6784.0 0.32817
## Total 53 20672.3 1.00000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1